Manuscript Model

Model Dataset

Model Data - West Only

Region N
Texas 3051
LA West 3656
MS Bight 1117
  • Total Number of Stations = 7824

  • Starting in 2000 and continuing through 2018

  • Total Sapidus Caught was 5468

  • Overall Frequency of Occurrence was 21.2

  • Overall Mean Catch Crabs/Hectare: 0.264

  • Overall Standard Error 0.018

  • Stations with no catch: 6167 / 7824 Stations or 78.82%

Annual Catch and Occurrence

Data Summary

NOTE: Contains Data Only from Western-Gulf Subset

Survey Year Stations Missing Obs % Occurrence Mean Catch SD Overdispersed
2000 491 0 0.1242363 0.1434330 0.7458628 yes
2001 416 0 0.1586538 0.4066819 2.5273291 yes
2002 513 0 0.2163743 0.3070619 1.4276630 yes
2003 477 0 0.2117400 0.3260161 1.3097278 yes
2004 440 0 0.1863636 0.2700141 1.1376114 yes
2005 430 0 0.3046512 0.7326053 4.4554998 yes
2006 392 0 0.2474490 0.2941062 1.2567796 yes
2007 401 0 0.2443890 0.3713497 2.1311305 yes
2008 513 0 0.1754386 0.1034162 0.3114427 no
2009 686 0 0.2172012 0.1905500 0.6311053 yes
2010 415 0 0.2554217 0.2344566 0.6430331 yes
2011 380 0 0.2842105 0.3323709 1.0015878 yes
2012 333 0 0.1561562 0.1029894 0.3033156 no
2013 274 0 0.1277372 0.0785191 0.3293913 yes
2014 349 0 0.2091691 0.2374299 1.6983507 yes
2015 350 0 0.2457143 0.2080342 0.6744467 yes
2016 322 0 0.2422360 0.1996629 0.5809559 yes
2017 335 0 0.2208955 0.2670072 0.8739255 yes
2018 307 0 0.1921824 0.1340553 0.4087250 yes

Annual Mean Catch

Annual Frequency of Occurrence

Side x Side

Region - Season Interactions

NOTE: Contains Data Only from Western-Gulf Subset

NOTE 2: Mean Catch (per hectare) calculated as the average crabs/hectare from each tow within a region-season grouping. Percent occurrence is calculated separately as the average annual percent occurrence for those same groups.

Factor Summary

Region Season Stations Missing Obs Mean Catch SD Overdispersed
Texas Summer 1559 0 0.2236771 0.9768701 yes
Texas Fall 1492 0 0.1062117 1.1289038 yes
LA West Summer 1874 0 0.5495995 2.6558490 yes
LA West Fall 1782 0 0.1885071 0.9017456 yes
MS Bight Summer 561 0 0.2561072 1.0760769 yes
MS Bight Fall 556 0 0.0857699 0.3310297 yes

Average frequency of occurrence for each region and season is calculated in two steps. In the first step the frequency of occurrence for each region and for both survey seasons is calculated for every year. In the second step those annual means are averaged to get an overall measure for each region for each season, and a measure of error around them is calculated to represent the inter-annual variation in the frequency of occurrence.

Region Season N Years % Occurrence % Occurrence SE
Texas Summer 19 0.2326514 0.0226426
Texas Fall 19 0.1012512 0.0152149
LA West Summer 19 0.3390328 0.0175933
LA West Fall 19 0.1692615 0.0223733
MS Bight Summer 19 0.2247988 0.0341018
MS Bight Fall 19 0.1329857 0.0209576

Mean Catch by Region and Season

Frequency of Occurrence

Side x Side

Candidate Models

Model Selection using AIC

Formulation AIC Delta AIC
no interactions 13813.95 250.2686
year * region 13671.18 107.5012
year * season 13714.15 150.4738
region * season 13814.66 250.9788
Year * region & year * season 13675.07 111.3977
all interactions 13563.68 0.0000

Predictor Significance

Predictor Df Deviance AIC LRT Pr(>Chi)
NA 3943.099 13561.68 NA NA
year_f 18 4030.280 13612.86 87.18098 0.0000000
region 2 3964.300 13578.88 21.20138 0.0000249
season 1 3950.663 13567.24 7.56352 0.0059562
year_f:region 36 4102.296 13648.87 159.19730 0.0000000
year_f:season 18 4032.022 13614.60 88.92312 0.0000000
region:season 2 3963.535 13578.11 20.43597 0.0000365

Percent Deviance Explained by Best Candidate Model: 22.83

Model Summary

Statistic reported below is the Wald Chi-Square z-score.

term estimate std.error statistic p.value
(Intercept) -2.5226968 3.318994e-01 -7.6007882 0.0000000
year_f2001 1.4475609 4.823366e-01 3.0011428 0.0026897
year_f2002 1.2997570 4.300605e-01 3.0222657 0.0025089
year_f2003 1.1551077 4.338772e-01 2.6622921 0.0077611
year_f2004 0.5951483 4.519179e-01 1.3169390 0.1878591
year_f2005 0.8261072 4.499882e-01 1.8358419 0.0663810
year_f2006 1.2248743 4.363714e-01 2.8069538 0.0050012
year_f2007 0.1928692 5.085116e-01 0.3792819 0.7044785
year_f2008 -0.0561732 4.682622e-01 -0.1199610 0.9045140
year_f2009 0.3721793 4.157922e-01 0.8951087 0.3707290
year_f2010 1.3678606 4.218076e-01 3.2428543 0.0011834
year_f2011 1.6862966 4.364890e-01 3.8633194 0.0001119
year_f2012 -0.3734306 5.004192e-01 -0.7462355 0.4555252
year_f2013 -1.0190240 6.012687e-01 -1.6947898 0.0901153
year_f2014 1.7698448 4.454852e-01 3.9728478 0.0000710
year_f2015 0.8857008 4.505800e-01 1.9656906 0.0493344
year_f2016 1.5388826 4.466982e-01 3.4450164 0.0005710
year_f2017 1.4514485 4.450963e-01 3.2609763 0.0011103
year_f2018 0.4645462 5.119802e-01 0.9073519 0.3642207
regionLA West 1.5939088 4.110403e-01 3.8777434 0.0001054
regionMS Bight -0.5343171 6.436653e-01 -0.8301164 0.4064730
seasonFall -1.6678533 6.317096e-01 -2.6402217 0.0082852
year_f2001:regionLA West -0.0313285 6.059282e-01 -0.0517034 0.9587650
year_f2002:regionLA West -0.7060823 5.435910e-01 -1.2989220 0.1939707
year_f2003:regionLA West -0.3861469 5.809924e-01 -0.6646333 0.5062850
year_f2004:regionLA West -0.1769451 5.663152e-01 -0.3124499 0.7546986
year_f2005:regionLA West 1.0925655 5.799504e-01 1.8838946 0.0595792
year_f2006:regionLA West -1.1332809 5.607124e-01 -2.0211446 0.0432648
year_f2007:regionLA West -0.4737498 6.227672e-01 -0.7607173 0.4468259
year_f2008:regionLA West -1.3075555 5.982034e-01 -2.1858043 0.0288299
year_f2009:regionLA West -0.5414312 5.223652e-01 -1.0364994 0.2999692
year_f2010:regionLA West -1.3877401 5.450823e-01 -2.5459277 0.0108988
year_f2011:regionLA West -1.4877185 5.662343e-01 -2.6273902 0.0086043
year_f2012:regionLA West -0.2031459 6.226694e-01 -0.3262501 0.7442352
year_f2013:regionLA West 0.1702608 7.134430e-01 0.2386466 0.8113796
year_f2014:regionLA West -2.2485507 5.804815e-01 -3.8735960 0.0001072
year_f2015:regionLA West -0.9289410 5.748246e-01 -1.6160426 0.1060851
year_f2016:regionLA West -2.0633657 5.722598e-01 -3.6056450 0.0003114
year_f2017:regionLA West -1.0354168 5.750724e-01 -1.8004981 0.0717820
year_f2018:regionLA West -0.9970019 6.394455e-01 -1.5591664 0.1189570
year_f2001:regionMS Bight -1.3446695 9.392252e-01 -1.4316796 0.1522355
year_f2002:regionMS Bight -0.6613078 8.518782e-01 -0.7762938 0.4375755
year_f2003:regionMS Bight 0.7718718 8.104769e-01 0.9523675 0.3409106
year_f2004:regionMS Bight -0.8048521 9.176103e-01 -0.8771176 0.3804227
year_f2005:regionMS Bight -23.0555869 2.509539e+04 -0.0009187 0.9992670
year_f2006:regionMS Bight 1.5413155 7.973287e-01 1.9330992 0.0532240
year_f2007:regionMS Bight 2.2531018 9.443265e-01 2.3859353 0.0170357
year_f2008:regionMS Bight -0.1661901 9.549289e-01 -0.1740340 0.8618387
year_f2009:regionMS Bight 2.2215266 7.548809e-01 2.9428836 0.0032517
year_f2010:regionMS Bight 0.6176639 9.930385e-01 0.6219939 0.5339459
year_f2011:regionMS Bight -0.8426081 1.008287e+00 -0.8356832 0.4033331
year_f2012:regionMS Bight 0.7996533 1.078004e+00 0.7417906 0.4582142
year_f2013:regionMS Bight 2.1630663 1.103177e+00 1.9607617 0.0499068
year_f2014:regionMS Bight -0.1870077 9.558497e-01 -0.1956455 0.8448877
year_f2015:regionMS Bight -0.8365878 1.101368e+00 -0.7595896 0.4474999
year_f2016:regionMS Bight -2.3816120 1.343394e+00 -1.7728324 0.0762565
year_f2017:regionMS Bight 0.5368907 9.321358e-01 0.5759791 0.5646293
year_f2018:regionMS Bight 0.6299970 1.058362e+00 0.5952567 0.5516719
year_f2001:seasonFall -1.0831173 8.627183e-01 -1.2554703 0.2093081
year_f2002:seasonFall -0.7111307 8.144259e-01 -0.8731681 0.3825715
year_f2003:seasonFall 1.0883988 7.521976e-01 1.4469586 0.1479085
year_f2004:seasonFall 0.0545197 8.184878e-01 0.0666102 0.9468920
year_f2005:seasonFall -0.1411545 8.121687e-01 -0.1737994 0.8620231
year_f2006:seasonFall -1.3370576 9.126945e-01 -1.4649564 0.1429328
year_f2007:seasonFall 3.9099502 7.882960e-01 4.9600027 0.0000007
year_f2008:seasonFall 1.4697352 8.113272e-01 1.8115196 0.0700605
year_f2009:seasonFall 0.1199549 7.775887e-01 0.1542652 0.8774007
year_f2010:seasonFall -0.0969826 7.845550e-01 -0.1236148 0.9016202
year_f2011:seasonFall 0.6176497 7.585877e-01 0.8142100 0.4155246
year_f2012:seasonFall 1.8216675 8.465341e-01 2.1519128 0.0314042
year_f2013:seasonFall 0.8779331 1.123718e+00 0.7812751 0.4346407
year_f2014:seasonFall 0.1221161 7.897130e-01 0.1546335 0.8771102
year_f2015:seasonFall 1.2693958 7.855777e-01 1.6158756 0.1061212
year_f2016:seasonFall 0.8072051 8.013457e-01 1.0073119 0.3137849
year_f2017:seasonFall -0.5217648 8.335876e-01 -0.6259267 0.5313630
year_f2018:seasonFall 0.7942303 8.601640e-01 0.9233475 0.3558261
regionLA West:seasonFall -1.4273364 8.168868e-01 -1.7472879 0.0805874
regionMS Bight:seasonFall 2.6392913 9.572109e-01 2.7572727 0.0058286
year_f2001:regionLA West:seasonFall 1.0743927 1.085168e+00 0.9900709 0.3221395
year_f2002:regionLA West:seasonFall 2.8183202 1.022460e+00 2.7564122 0.0058439
year_f2003:regionLA West:seasonFall 1.1596534 9.934722e-01 1.1672731 0.2431001
year_f2004:regionLA West:seasonFall 2.2717123 1.033221e+00 2.1986708 0.0279013
year_f2005:regionLA West:seasonFall 1.6319522 1.027383e+00 1.5884555 0.1121834
year_f2006:regionLA West:seasonFall 3.1233229 1.191337e+00 2.6216954 0.0087494
year_f2007:regionLA West:seasonFall -1.3797323 1.016559e+00 -1.3572576 0.1746994
year_f2008:regionLA West:seasonFall 2.1041048 1.028964e+00 2.0448778 0.0408669
year_f2009:regionLA West:seasonFall 1.2507351 9.999241e-01 1.2508301 0.2109965
year_f2010:regionLA West:seasonFall 2.1773613 1.014205e+00 2.1468653 0.0318040
year_f2011:regionLA West:seasonFall 2.1129189 9.932891e-01 2.1271943 0.0334039
year_f2012:regionLA West:seasonFall -0.3379970 1.119827e+00 -0.3018295 0.7627820
year_f2013:regionLA West:seasonFall 0.9674971 1.378100e+00 0.7020516 0.4826470
year_f2014:regionLA West:seasonFall 2.6464584 1.028604e+00 2.5728655 0.0100860
year_f2015:regionLA West:seasonFall 0.9123447 1.028351e+00 0.8871919 0.3749756
year_f2016:regionLA West:seasonFall 0.8770735 1.070046e+00 0.8196597 0.4124102
year_f2017:regionLA West:seasonFall 0.6889676 1.122341e+00 0.6138667 0.5393034
year_f2018:regionLA West:seasonFall 1.5625355 1.098167e+00 1.4228583 0.1547772
year_f2001:regionMS Bight:seasonFall -0.6658444 1.471203e+00 -0.4525850 0.6508476
year_f2002:regionMS Bight:seasonFall -0.6443478 1.294920e+00 -0.4975966 0.6187684
year_f2003:regionMS Bight:seasonFall -4.9358899 1.276094e+00 -3.8679664 0.0001097
year_f2004:regionMS Bight:seasonFall 0.2358027 1.624922e+00 0.1451163 0.8846191
year_f2005:regionMS Bight:seasonFall 23.4467784 2.509539e+04 0.0009343 0.9992545
year_f2006:regionMS Bight:seasonFall -1.8844192 1.315935e+00 -1.4319998 0.1521439
year_f2007:regionMS Bight:seasonFall -6.4670075 1.329080e+00 -4.8657767 0.0000011
year_f2008:regionMS Bight:seasonFall -2.6549459 1.396063e+00 -1.9017371 0.0572055
year_f2009:regionMS Bight:seasonFall -4.2973049 1.285840e+00 -3.3420225 0.0008317
year_f2010:regionMS Bight:seasonFall -2.4745921 1.491515e+00 -1.6591135 0.0970929
year_f2011:regionMS Bight:seasonFall -2.6720578 1.582227e+00 -1.6887952 0.0912587
year_f2012:regionMS Bight:seasonFall -2.6213922 1.639367e+00 -1.5990273 0.1098145
year_f2013:regionMS Bight:seasonFall -3.4408723 1.983350e+00 -1.7348794 0.0827622
year_f2014:regionMS Bight:seasonFall -2.9338609 1.558110e+00 -1.8829614 0.0597056
year_f2015:regionMS Bight:seasonFall -3.2090400 1.796716e+00 -1.7860585 0.0740898
year_f2016:regionMS Bight:seasonFall -23.4575078 4.058982e+04 -0.0005779 0.9995389
year_f2017:regionMS Bight:seasonFall -1.9693608 1.485972e+00 -1.3253011 0.1850713
year_f2018:regionMS Bight:seasonFall -2.3765912 1.608082e+00 -1.4779040 0.1394335

Interaction Plots

Tukey HSD multiple comparison test

Test 1. Region

## 
##   Simultaneous Tests for General Linear Hypotheses
## 
## Multiple Comparisons of Means: Tukey Contrasts
## 
## 
## Fit: MASS:::glm.nb(formula = sapidus_catch ~ year_f * region * season + 
##     offset(log(area_hectares)), data = seamap_west, init.theta = 0.174655286, 
##     link = log)
## 
## Linear Hypotheses:
##                         Estimate Std. Error z value Pr(>|z|)    
## LA West - Texas == 0      1.5939     0.4110   3.878 0.000297 ***
## MS Bight - Texas == 0    -0.5343     0.6437  -0.830 0.678372    
## MS Bight - LA West == 0  -2.1282     0.6024  -3.533 0.001058 ** 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)

Test 2. Year

## 
##   Simultaneous Tests for General Linear Hypotheses
## 
## Multiple Comparisons of Means: Tukey Contrasts
## 
## 
## Fit: MASS:::glm.nb(formula = sapidus_catch ~ year_f * region * season + 
##     offset(log(area_hectares)), data = seamap_west, init.theta = 0.174655286, 
##     link = log)
## 
## Linear Hypotheses:
##                    Estimate Std. Error z value Pr(>|z|)   
## Fall - Summer == 0  -1.6679     0.6317   -2.64  0.00829 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)

Catch per Hectare Plot

Seasonal Prediction Differences

Observed vs. Predicted Data

Original

Predictions Only

Observed Only

Raster Plots

NOTE: Contains Data Only from Western-Gulf Subset

Statistical Zones

Sampling Effort

Catch per Hectare

Variance in CPUE

Total Catch

Outlining Cells with Geom_Tile

Study Area Size From Convex Hull

## [1] "Area of Analysis Data Study Area (raster): 122297.8 km2"
## [1] "Area of Analysis Data Study Area (raster): 12229780 Hectares"